EHPCC: Software

Welcome
A goal of the EHPCC is to provide access to software which can take advantage of a clustered environment thus facilitating the rapid generation of meaningful data. We currently software which allows for neural simulation, sequence and genome analysis, statistical computing and algorithim development and numerical computation. There is also support for parellel programming development via the MPICH and PVM libraries and development tools. Following is a selected list of supported applications. If you are interested in requesting support for a particulalr application then please contact us to determine its suitability for use on the cluster. For information on how to submit and manage jobs on the cluster , please consult our pages on Sun Grid Engine.

Neural Simulation

GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform which was developed to support the simulation of neural systems ranging from complex models of single neurons to simulations of large networks made up of more abstract neuronal components.GENESIS has provided the basis for laboratory courses in neural simulation at Caltech, the Marine Biological Laboratory, the Crete, Trieste, Bangalore, and Obidos short courses in Computational Neuroscience, and at least 49 universities of which we are aware. Most current GENESIS applications involve realistic simulations of biological neural systems.

Sequence And Genomic Analysis

BLAST (Basic Local Alignment Search Tool) allows biologists to query target databases of DNA or protein seqeunces. The query is also a set of DNA or protein seqeunces. Rigorous statistics are used to identify statistically significant matches which helps to direct experimental design and to locate and/or prove function of the query seqeunce. BLAST also has application in the comparison of complete genomes as a means to identify similaritites and difference among organisms. We offer three BLAST distributions - 1) the primary NCBI distribution, 2) the Washington University "WU-BLAST", and 3) MPI-BLAST which is special implementation of the BLAST algorithm specifically for true parallel environments. Please see the "What is BLAST" tutorial for more details on how BLAST accomplishes its work.

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by the program cross_match, an efficient implementation of the Smith-Waterman-Gotoh algorithm.

Statistical Computing

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.